new: Relative Codon Bias Score

models/calc_RCBS.m

@@ -0,0 +1,57 @@
+function RCBS = calc_RCBS(seq)
+% compute the Relative Codon Bias Score (Roymondal, 2009)
+%
+% Alon Diament, Tuller Lab, August 2014.
+
+if iscell(seq)
+    RCBS = cellfun(@calc_RCBS, seq);
+    return;
+end
+
+CodonCount = cell2mat(struct2cell(codoncount(seq))); % sorted
+P = CodonCount / sum(CodonCount);
+BCC = calc_BCC(calc_BNC(seq)); % background codon composition
+D = (P - BCC) ./ BCC; % per-codon score
+
+nz = P~=0;
+RCBS = log(1 + D(nz)') * CodonCount(nz) / sum(CodonCount);
+RCBS = exp(RCBS) - 1; % gene score
+end
+
+
+function [BNC, NTs] = calc_BNC(back_seq)
+% background nucleotide composition (BNC)
+
+BNC = zeros(4,3); % 4-NTs x 3-positions
+NTs = {'A','C','G','T'};
+
+for pos = 1:3
+    seq = back_seq(pos:3:end);   
+    % derive NT distibution directly
+    for nt = 1:4
+        BNC(nt, pos) = sum(seq == NTs{nt}) / length(seq);
+    end
+end
+end
+
+
+function BCC = calc_BCC(BNC)
+% background codon composition (BCC)
+% given the background nucleotide composition (BNC)
+
+BCC = zeros(64,1);
+i = 0;
+
+for n1 = 1:4
+    f(1) = BNC(n1,1);
+    for n2 = 1:4
+        f(2) = BNC(n2,2);
+        for n3 = 1:4
+            f(3) = BNC(n3,3);
+            % codon probability is f(1)*f(2)*f(3)
+            i = i + 1;
+            BCC(i) = f(1)*f(2)*f(3);
+        end
+    end
+end
+end